Nuclear receptors represent a superfamily of proteins that specifically bind physiologically relevant small molecules, such as hormones, vitamins, fatty acids or the like. Binding of an agonist to a nuclear receptor, induces the receptor to modulate transcription in the cell in a positive or negative way (the receptor-agonist complex can have transcription independent actions as well.). Unlike integral membrane receptors and membrane associated receptors, nuclear receptors mostly reside in either the cytoplasm or nucleus of eukaryotic cells. Thus, nuclear receptors comprise a class of intracellular, soluble, ligand-regulated transcription factors.
The biology and physiology of several nuclear receptors has been worked out in some detail. For example, the physiological and molecular basis of thyroid hormone action is reviewed in Yen (2001) “Physiological and Molecular Basis of Thyroid Hormone Action” Physiological Reviews 81(3):1097-1142, and the references cited therein. Known and well characterized nuclear receptors include those for glucocorticoids (GRs), androgens (ARs), mineralocorticoids (MRs), progestins (PRs), estrogens (ERs), thyroid hormones (TRs), vitamin D (VDRs), retinoids (RARs and RXRs), and the peroxisome proliferator activated receptors (PPARs) that bind eicosanoids. The so called “orphan receptors” are also part of the nuclear receptor superfamily, as they are structurally homologous to classic nuclear receptors, such as steroid and thyroid receptors. Ligands have not been identified for orphan receptors but it is likely that small molecule ligands will be discovered in the near future for many of this class of transcription factors. Generally, nuclear receptors specifically bind physiologically relevant small molecules with high affinity. Apparent Kd's are commonly in the 0.01-20 nM range, depending on the nuclear receptor/ligand pair.
Nuclear receptors are involved in a myriad of physiological processes and medical conditions such as hypertension, heart failure, atherosclerosis, inflammation, immunomodulation, hormone dependent cancers (e.g. breast, thyroid, and prostate cancer), modulation of reproductive organ function, hyperthyroidism, hypercholesterolemia and other abnormalities of lipoproteins, diabetes, osteoporosis, mood regulation, mentation, and obesity. Consequently, it is advantageous to develop ligands to nuclear receptors with desired properties, e.g., activating the receptor, deactivating the receptor, etc.
Certain progress has been made in this regard. For example, U.S. Pat. No. 5,883,294 by Scanlan et al. (SELECTIVE THYROID HORMONE ANALOGUES) describes, e.g., several classes of artificial thyroid hormone receptor ligands. Similarly, U.S. Pat. No. 6,266,622 by Scanalan et al. (NUCLEAR RECEPTOR LIGANDS AND LIGAND BINDING DOMAINS) also describes several classes of thyroid hormone receptor ligands. For example, superagonists are described in the '622 patent, in which, e.g., the interactions of the ligand with various receptor residues (e.g., Arg 262, Arg 266 and Arg 228) in the ligand binding pocket are optimized. The '622 patent also provides methods of designing antagonists to thyroid hormone and other nuclear receptors, via the extension hypothesis, which provides, in part, that various bulky extension groups on receptor ligands confer antagonistic activity to the ligand. For example, extension groups that project towards the C terminal helix of the receptor, when the ligand is bound to the receptor, can provide antagonist activity.
The present invention derives, in part, from the surprising discovery that certain extension groups can be used in agonist design. This and many other features of the invention, will become apparent upon review of the following.